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File

tripal_feature/includes/gff_loader.inc, line 931

@todo Add file header description

Code

function tripal_feature_load_gff3_derives_from($feature, $subject, $organism) {

  // get the subject type
  $values = array(
    'organism_id' => $organism->organism_id,
    'uniquename' => $subject,
  );
  $options = array('statement_name' => 'sel_tripalgfftemp_orun');
  $result = tripal_core_chado_select('tripal_gff_temp', array('type_name'), $values, $options);
  if (count($result) == 0) {
    watchdog("T_gff3_loader", "Cannot find subject type for feature in 'derives_from' relationship: %subject", array('%subject' => $subject), WATCHDOG_WARNING);
    return '';
  }
  $subject_type = $result[0]->type_name;

  // get the subject feature
  $match = array(
    'organism_id' => $organism->organism_id,
    'uniquename' => $subject,
    'type_id' => array(
      'name' => $subject_type,
      'cv_id' => array(
        'name' => 'sequence'
      ),
    ),
  );
  $options = array('statement_name' => 'sel_feature_orunty');
  $sfeature = tripal_core_chado_select('feature', array('feature_id'), $match, $options);
  if (count($sfeature) == 0) {
    watchdog('T_gff3_loader', "Could not add 'Derives_from' relationship " .
      "for %uniquename and %subject.  Subject feature, '%subject', " .
      "cannot be found", array('%uniquename' => $feature->uniquename, '%subject' => $subject), WATCHDOG_ERROR);
    return;
  }

  // now check to see if the relationship already exists
  $values = array(
    'object_id' => $sfeature[0]->feature_id,
    'subject_id' => $feature->feature_id,
    'type_id' => array(
      'cv_id' => array(
        'name' => 'relationship'
      ),
      'name' => 'derives_from',
    ),
    'rank' => 0
  );
  $options = array('statement_name' => 'sel_featurerelationship_objectid_subjectid_typeid_rank');
  $rel = tripal_core_chado_select('feature_relationship', array('*'), $values, $options);
  if (count($rel) > 0) {
    return;
  }

  // finally insert the relationship if it doesn't exist
  $options = array('statement_name' => 'ins_featurerelationship_objectid_subjectid_typeid_rank');
  $ret = tripal_core_chado_insert('feature_relationship', $values, $options);
  if (!$ret) {
    watchdog("T_gff3_loader", "Could not add 'Derives_from' relationship for $feature->uniquename and $subject", 
    array(), WATCHDOG_WARNING);
  }
}